Abstract Soil microbial biomass plays a key role in the biogeochemical cycles, degradation of organic pollutants and soil aggregation, and its estimation through soil microbial biomass-C (MB-C) is often referred as a potential indicator of soil functioning. This study aimed to identify reference values of MB-C that would relate to crop yield. Soybean and maize grain yields and microbial biomass-C (MB-C) data were gathered from studies listed in “Web of Science” performed in agroecosystems located in the Atlantic Forest Biome in Southern Brazil. Database was composed by 78 datasets, where soil samplings for evaluation of MB-C were performed at the 0–10 cm layer at flowering stage, and evaluated by the fumigation-extraction method. A meta-regression using the Mitscherlich model was applied to determine the MB-C reference value corresponding to 80% of maximum yield. The effects of soil management systems and crop systems were verified by comparing the confidence intervals. Soil tillage decreased MB-C and yield, while crop rotation increased yield but not MB-C. It was not possible to find a reference value for soybean, because of the variability not explainable by the MB-C. The reference value related to high maize yield (>6,752 kg ha−1) was of 170 μg C g−1 soil, but further results must be included to decrease the variability.